Introduction of small interfering RNAs (siRNAs) into cells with transfection reagents results in efficient gene silencing. Unfortunately, while siRNA-based functional genomics is widely used in vitro, the ability to apply this technology to primary cells and in vivo target validation has been impeded limited availability of efficient and non-toxic delivery systems. We, in collaboration with RXi Pharmaceuticals, have developed a novel class of covalently modified RNAi compounds that do not require a delivery vehicle to enter cells and have improved pharmacology compared to traditional siRNAs. We term these compounds "self- delivering RNA" or sdRNA. sdRNA is a hydrophobically modified RNAi- antisense hybrid, which has been demonstrated to be highly efficacious in vitro in primary cells and in vivo upon local administration. Robust uptake and/or silencing without toxicity has been demonstrated in several tissues including dermal, muscle, tumors, alveolar macrophages, spinal cord, retina etc. In dermal layer and retina, intradermal and intravitreal injections of sdRNA at 5g doses induce potent and long lasting silencing. RXi has utilized extensive screening to successfully identify functional sdRNA compounds against a number of targets and are actively procuring some of these compounds toward clinical development. A major hurdle to commercialization of sdRNA as a superior functional genomics tool, enabling RNAi in primary cells and in vivo, is the relatively low hit rate as compared to conventional siRNAs. While the need to screen large number of sequences per gene is not a limiting factor for therapeutic applications, it severely limits the applicability of sdRNA technology to functional genomics, where cost effective compound selection against thousands of genes is required. The objective of this proposal is to optimize sdRNA structure, chemistry, targeting position, sequence preferences to develop an algorithm for sdRNA potency prediction. Completion of this project will create a foundation for developing the first line of sdRNAs based products for commercialization, which will be done as part of phase II proposal. Availability of these sdRNA reagents that are active in all cell types and in vivo will enable functional genomics and target stratification/validation studies and have a major impact on the drug discovery process. PUBLIC HEALTH RELEVANCE: The utility of RNAi technology is severely limited by limited availability of efficient delivery of RNAi compounds to primary cells and in vivo. We have recently developed a new class of RNAi compounds, "self- delivering rxRNA" or sdRNA. sdRNA is a hydrophobically modified RNAi- antisense hybrid, which has been demonstrated to be highly efficacious in vitro in primary cells and in vivo upon local administration. Current proposal will focus on further optimizing this new class of compounds to enable rapid design and synthesis.